Tool: gprofileR
net_dir = "/pastel/projects/speakeasy_dlpfc/SpeakEasy_net_MF/"
modules_file = read.table(paste0(net_dir, "geneBycluster.txt"), header = T)We removed the clusters with < 30 nodes for downstream analysis.
modules_file = modules_file[, c("symbol", "cluster_lv3")]
modules_file$module_clusters = paste0("m", modules_file$cluster_lv3)
modules_file$cluster_lv3 = NULL
modules_size = as.data.frame(table(modules_file$module_clusters))
colnames(modules_size) = c("module", "n_nodes")
createDT(modules_size)sessionInfo()R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 8
Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.12.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] DT_0.20 plotly_4.10.0 ggplot2_3.3.5 knitr_1.37
[5] gprofiler2_0.2.1
loaded via a namespace (and not attached): [1] tidyselect_1.1.2 xfun_0.29 bslib_0.3.1 purrr_0.3.4
[5] colorspace_2.0-3 vctrs_0.3.8 generics_0.1.2 htmltools_0.5.2
[9] viridisLite_0.4.0 yaml_2.3.5 utf8_1.2.2 rlang_1.0.1
[13] later_1.3.0 jquerylib_0.1.4 pillar_1.7.0 glue_1.6.1
[17] withr_2.4.3 DBI_1.1.2 lifecycle_1.0.1 stringr_1.4.0
[21] munsell_0.5.0 gtable_0.3.0 htmlwidgets_1.5.4 evaluate_0.15
[25] fastmap_1.1.0 httpuv_1.6.5 crosstalk_1.2.0 fansi_1.0.2
[29] Rcpp_1.0.8 xtable_1.8-4 promises_1.2.0.1 scales_1.1.1
[33] jsonlite_1.7.3 mime_0.12 digest_0.6.29 stringi_1.7.6
[37] shiny_1.7.1 dplyr_1.0.8 grid_4.1.2 cli_3.2.0
[41] tools_4.1.2 bitops_1.0-7 magrittr_2.0.2 sass_0.4.0
[45] lazyeval_0.2.2 RCurl_1.98-1.6 tibble_3.1.6 crayon_1.5.0
[49] tidyr_1.2.0 pkgconfig_2.0.3 ellipsis_0.3.2 data.table_1.14.2 [53] assertthat_0.2.1 rmarkdown_2.11 httr_1.4.2 rstudioapi_0.13
[57] R6_2.5.1 compiler_4.1.2